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gbouras13 / pharokka

fast phage annotation program
MIT License
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Inquiry on Pharokka #342

Closed songmj86 closed 2 months ago

songmj86 commented 2 months ago

Inquiry

Hi

I would like to ask any plan or possibility that Pharokka will attemps to use prodigal-gv for virus-specific gene calling and KEGG numbers to annotate genes as class I and II AMG (https://www.sciencedirect.com/science/article/pii/S1369527416300376)

Thanks for developing such a nice tool !

Best regards

songmj86 commented 2 months ago

Hi !

I apologize first that pharokka uses prodigal-gv for gene calling.

What I want to ask you was indeed that "is there any plan to use CDS as inputs as some of my genes need to be structually called as either single or meta mode for prodigal-gv (Pharokka does not seem to distinguish the parameters)" ??

Thanks !

gbouras13 commented 2 months ago

Hi @songmj86 ,

prodigal-gv must be run in meta-mode always (to incorporate the alternative genetic code models) - there is no way to specify single mode.

And thank you for that link - Pharokka doesn't support Class I/II AMGs (yet) but I will have a read and consider adding it!

George

songmj86 commented 2 months ago

Oh! Thanks for quick response!